Aim: To evaluate the sealing ability of mineral trioxide aggregate (MTA) and resin-modified glass ionomer cement (RMGIC) to seal the furcal perforation with and without internal matrix. Materials and methods: Sixty freshly extracted intact human permanent mandibular molars were selected. After creating furcal perforation, the teeth were randomly divided into four experimental groups containing 15 teeth each according to the furcal perforation repair materials used. Group I—RMGIC without internal matrix. Group II—RMGIC with internal matrix. Group III—MTA without internal matrix. Group IV—MTA with internal matrix. To evaluate the sealing ability of furcal perforation, dye extraction method was performed using 2% methylene blue dye and 65% concentrated nitric acid. Spectrophotometer was used for measuring dye absorbance at 550 nm. Results: Group I (RMGIC without internal matrix) showed highest microleakage followed by group II (RMGIC with internal matrix), group III (MTA without internal matrix), and group IV (MTA with internal matrix). There was a significant difference found between group I and group II, but there was no significant difference seen between group III and group IV. Conclusion: Mineral trioxide aggregate has excellent sealing ability and can be used with and without internal matrix in repair of furcation perforation. Resin-modified glass ionomer cement should be used with internal matrix to repair furcation perforations. Clinical significance: Mineral trioxide aggregate with and without internal matrix whereas RMGIC with internal matrix have been successfully used in repair of furcation perforation.